Managers 12Sept07

From GO Wiki
Revision as of 12:30, 30 June 2014 by Gail (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

GO Managers, Weds. Sept. 12 8 AM PDT / 10 AM CDT / 11 AM EDT / 4 PM BST

Agenda/chair: David
Minutes: Eurie
Present: Chris, David, Eurie, Jen, Judy, Midori, Pascale, Suzi

Review Action Items from previous meeting

Carried over from Aug. 29:

  • Chris: Add replaced_by & consider tags to database

Now in the schema and loading code is there. There is a follow up to-do item to get AmiGO to display the tags.

  • Chris: Write abstract for Biocurator meeting

Will do it today.

  • Individual managers: Fill in progress report for SAB.

Progress report available as a wiki page - it's under resources available for the GO Resource. There was slight preference for editing a Word document. Judy will also provide a link to download the Word document from the wiki. And she will send it out to the managers list so that we can edit the word document as a group.

  • Managers: Have a look at the schedule on the wiki for the Princeton meetings. Comment where appropriate.
    • The 9-year time line should be done among PIs. They can report back but there should be some preliminary discussion.
    • Before the meeting, everyone look for their name and try to prune the list of action items before the start of the meeting. All the action items will be put on the wiki
    • Judy will add an advocacy item to the agenda.
    • Will the PI leads on the aims or the managers do the presentation? PIs will discuss on the call that immediately follows.
    • Progress reports at GOC meeting should parallel the progress reports at the SAB meeting.
    • SAB meeting: we will divide into quarters and present progress and future plans at the same time. If there are issues being discussed, then it can be earmarked for further discussion in the afternoon.
    • GOC meeting: we will divide into quarters and only present progress information.
    • Managers should take a look and suggest organization of the meeting. Also, if there are wiki pages that provide background information, managers should link these pages from the agenda item.

Individual Manager reports

Ontology Development

  • David working on "regulates"
  • Muscle and Cardio changes should be committed within 2 months.


  • Flowcharts almost ready to be linked to live website:
  • Erika Feltrin of CRIBI attended the SIGA meeting ( Summary SIGA course on Bioinformatics tools for the analysis and the management of the data of sequence, genomic annotation and gene expression. She and Giorgio Valle gave a 1 day tutorial on GO ontology development and annotation.


  • Many database extensions
  • consider and replaced_by tags, synonym_types
  • Gene product counts precomputed by species and data source so can be
  • Putting taxon information in the database
  • gp2protein reports - what's missing and
  • new release of go-perl on CPAN
  • cross-product guide on wiki
  • requirements for ID mapping on wiki
  • John has filter queries in OBO-edit
  • more documentation available on OBO XML

Reference Genomes

  • There was a phone conference yesterday going over the agenda.

User Advocacy

  • Interactome meeting report

Lots of ideas from Ewan Birney. Peter is coming for the GOC meeting so Jen will list issues on the wiki.

  • What in the world is moodle?

The EBI has funding to use a company that produces teaching materials. If we make up word docs with screen shots and the text of the voice over the EBI will pay the company to turn these into flash tutorials with voice over, printable pdf tutorials and online html tutorials. It will be quite a lot of work to make up the word docs to give to them, but this is all we have to do. For groups like GO that are partly, but not wholely, in the EBI the material will be branded with all the groups logos rather than just the EBI logo.
Q:Should we adopt this as our outlet for teaching materials so as to justify the time spent and maximize the benefit of having the EBI funded manpower?
A: yes, but we should check the resulting materials very carefully.


  • GOC, SAB, Reference Genome meetings
  • PAG (plant & animal genomes)
  • BioCurator meeting in October
  • Judy attending Mammalian Genome meeting in Kyoto in October

Staffing and Personnel

  • New Dicty programmer starting in end of October.


  • NAR update due middle of Sept. Midori is coordinating. Who should we include on the GOC (members, associates, or whatever) list. We're also supposed to suggest six possible referees, any suggestions?
    • Authors list: Be inclusive and remove the bit of text preceding the actual names and affiliations.
    • Acknowledgement about funding for the GOC groups: Put all groups' funding information in.
    • Chris will give reference for the SPARQL reference
    • Referees: Chris Stoeckert, Ken Fukuda, Richard Schuerman, Lindsey Cowell, Oliver Hoffman, Bill Bug, Phil Lord

Other Current Topics and Concerns